I have constructed a MSA, but I observed that certain part in the alignment has a large gaps due to the presence of unconserved region of a protein. I wish to remove that part of the protein by replacing those unconserved region with symbol // . Is there any tool with such function? Currently I am using GeneDoc, but the sequence location indicator automatically substracted when I removed that region in residue edit mode. Is this normal for a MSA? I thought the sequence location indicator should remain same (or increase due to participation of remaining sequence) even if I removed that region.
Edited by dcch, 31 October 2012 - 11:20 PM.